This applies to both v1.2.9 and the latest Linux build Slic3r-1.3.0-dev-451f2e3-x86_64.AppImage. Workaround is to split the file into multiple objects using the Split command in Slic3r. But without doing a preview, there's no way to know that the split is needed. In case it's relevant, the STL was generated using OpenSCAD (version 2017.10.18.nightly (git 995fac0).

I get exactly the same thing with Simplify3D even though it rearranged the parts on the build plate. The reason is that the part that is out of the outline is sitting slightly above the bed and doesn't start printing until the second layer. Check your OpenScad model.